QianhuiXu
commented
2 years ago @leeanapeters Hi, I have the same problem.
This is my code:
motifs = runHomer(
- x.sp[,idy,"pmat"],
- mat = "pmat",
- path.to.homer = "/home/qianhui/anaconda3/envs/chipseq/share/homer/bin/findMotifsGenome.pl",
- result.dir = "./homer/DoubleNegativeTcell",
- num.cores=5,
- genome = 'hg19',
- motif.length = 10,
- scan.size = 300,
- optimize.count = 2,
- background = 'automatic',
- local.background = FALSE,
- only.known = TRUE,
- only.denovo = FALSE,
- fdr.num = 5,
- cache = 100,
- overwrite = TRUE,
- keep.minimal = FALSE
- );
Here is the error:
Position file = ./homer/DoubleNegativeTcell/target_7d9156c7a25
Genome = hg19
Output Directory = ./homer/DoubleNegativeTcell
Motif length set at 10,
Fragment size set to 300
Will optimize 2 putative motifs
Using 5 CPUs
Using 100 MB for statistics cache
Will randomize and repeat motif finding 5 times to estimate FDR
Will not run homer for de novo motifs
Found mset for "human", will check against vertebrates motifssh: 1: bed2pos.pl: not found sh: 1: checkPeakFile.pl: not found sh: 1: cleanUpPeakFile.pl: not found ls: cannot access '/home/qianhui/anaconda3/envs/chipseq/share/homer/.//data/genomes/hg19//preparsed//hg19.*.cgbins': No such file or directory Could not find background files for 300 bp fragments Below are the sizes that are already available prepared. HOMER will now create background files for 300 bp fragments To CANCEL and rerun with a differet "-size <#>", hit <CTRL+C> now! 5 4 3 2 1 Preparsing genome for 300 bp fragments...(will probably take 1-5 min) sh: 1: preparseGenome.pl: not found wc: /home/qianhui/anaconda3/envs/chipseq/share/homer/.//data/genomes/hg19//preparsed//hg19.300.gcbins: No such file or directory Use of uninitialized value $lineCount in numeric lt (<) at /home/qianhui/anaconda3/envs/chipseq/share/homer/bin/findMotifsGenome.pl line 648. !!!! Might have something wrong with preparsed files !!!! Rerun and add "-preparse" to the command line to force recreation of the files sh: 1: resizePosFile.pl: not found sh: 1: homerTools: not found sh: 1: cleanUpSequences.pl: not found sh: 1: removePoorSeq.pl: not found
Not removing redundant sequencessh: 1: homerTools: not found sh: 1: freq2group.pl: not found
Total sequences set to 50000
Choosing background that matches in CpG/GC content...wc: /home/qianhui/anaconda3/envs/chipseq/share/homer/.//data/genomes/hg19//preparsed//hg19.300.gcbins: No such file or directory cat: /home/qianhui/anaconda3/envs/chipseq/share/homer/.//data/genomes/hg19//preparsed//hg19.300.gcbins: No such file or directory sh: 1: makeBinaryFile.pl: not found sh: 1: randRemoveBackground.pl: not found sh: 1: assignGeneWeights.pl: not found Assembling sequence file... sh: 1: filterListBy.pl: not found Normalizing lower order oligos using homer2 sh: 1: homer2: not found Finished preparing sequence/group files
----------------------------------------------------------
Known motif enrichmentsh: 1: findKnownMotifs.pl: not found Skipping... Job finished - if results look good, please send beer to ..
Cleaning up tmp files...Error in file(file, "rt") : cannot open the connection In addition: Warning message: In file(file, "rt") : cannot open file './homer/DoubleNegativeTcell/knownResults.txt': No such file or directory
Please let me know the solution of the problem. Thank you very much!
ljohanam
Hi, thanks for a great package!
I am having some issues when trying to perform runHomer for motif discovery across my clusters.
Here is the code I ran
motifs = runHomer( CD8.sp[,idy.ls[["1"]],"pmat"], mat = "pmat", path.to.homer = "/Volumes/LDP/homer/bin//findMotifsGenome.pl", result.dir = "./homer/C1", num.cores=5, genome = 'hg38', motif.length = 10, scan.size = 200, optimize.count = 2, background = 'automatic', local.background = FALSE, only.known = TRUE, only.denovo = FALSE, fdr.num = 5, cache = 100, overwrite = TRUE, keep.minimal = FALSE );
Here is the output/error: h: bed2pos.pl: command not found sh: checkPeakFile.pl: command not found sh: cleanUpPeakFile.pl: command not found ls: /Volumes/LDP/homer//data/genomes/hg38//preparsed//hg38.*.cgbins: No such file or directory Could not find background files for 200 bp fragments Below are the sizes that are already available prepared. HOMER will now create background files for 200 bp fragments To CANCEL and rerun with a differet "-size <#>", hit <CTRL+C> now! 5 4 3 2 1 Preparsing genome for 200 bp fragments...(will probably take 1-5 min) sh: preparseGenome.pl: command not found wc: /Volumes/LDP/homer//data/genomes/hg38//preparsed//hg38.200.gcbins: open: No such file or directory Use of uninitialized value $lineCount in numeric lt (<) at /Volumes/LDP/homer/bin/findMotifsGenome.pl line 648. !!!! Might have something wrong with preparsed files !!!! Rerun and add "-preparse" to the command line to force recreation of the files sh: resizePosFile.pl: command not found sh: homerTools: command not found sh: cleanUpSequences.pl: command not found sh: removePoorSeq.pl: command not found
sh: homerTools: command not found sh: freq2group.pl: command not found
wc: /Volumes/LDP/homer//data/genomes/hg38//preparsed//hg38.200.gcbins: open: No such file or directory cat: /Volumes/LDP/homer//data/genomes/hg38//preparsed//hg38.200.gcbins: No such file or directory sh: makeBinaryFile.pl: command not found sh: randRemoveBackground.pl: command not found sh: assignGeneWeights.pl: command not found Assembling sequence file... sh: filterListBy.pl: command not found Normalizing lower order oligos using homer2 sh: homer2: command not found Finished preparing sequence/group files
sh: findKnownMotifs.pl: command not found Skipping... Job finished - if results look good, please send beer to ..
Error in file(file, "rt") : cannot open the connection In addition: Warning message: In file(file, "rt") : cannot open file './homer/C1/knownResults.txt': No such file or directory
I've made sure to add the path to homer in my bash_profile and when I call echo $PATH I see the path listed correctly.
Any help would be much appreciated! Thanks! (I am using R 3.6.3 on Mac high Sierra)